is this related to itemcreate.2da (which wasn't included in the download) or baseitems.2da (which I did install another mod that effects it, but it was the Republic Uniforms for K2 by JC, so in theory USM shouldn't be effected)?

Yes.

We chose not to make models for each Lightsaber type so we created new Crystals in baseitems.2da.

I'm not familar with Republic Uniforms mod but I'm thinking it might be easyer to use the USM baseitems then edit it for the other mod. Or choose one mod.